Simultaneous modeling of multiple loops in proteins

Protein Science : a Publication of the Protein Society
D Rosenbach, R Rosenfeld

Abstract

The most reliable methods for predicting protein structure are by way of homologous extension, using structural information from a closely related protein, or by "threading" through a set of predefined protein folds ("inverse folding"). Both sets of methods provide a model for the core of the protein--the structurally conserved secondary structures. Due to the large variability both in sequence and size of the loops that connect these secondary structures, they generally cannot be modeled using these techniques. Loop-closure algorithms are aimed at predicting loop structures, given their end-to-end distance. Various such algorithms have been described, and all have been tested by predicting the structure of a single loop in a known protein. In this paper we propose a method, which is based on the bond-scaling-relaxation loop-closure algorithm, for simultaneously predicting the structures of multiple loops, and demonstrate that, for two spatially close loops, simultaneous closure invariably leads to more accurate predictions than sequential closure. The accuracy of the predictions obtained for pairs of loops in the size range of 5-7 residues each is comparable to that obtained by other methods, when predicting the structures of ...Continue Reading

References

Jan 1, 1992·Protein Science : a Publication of the Protein Society·N Horton, M Lewis
Oct 5, 1992·Journal of Molecular Biology·V N Maiorov, G M Crippen
Jul 2, 1992·Nature·D T JonesJ M Thornton
Jul 20, 1991·Journal of Molecular Biology·C WilsonD A Agard
Sep 5, 1991·Journal of Molecular Biology·B K Shoichet, I D Kuntz
Aug 20, 1987·Journal of Molecular Biology·C Chothia, A M Lesk
Aug 1, 1993·Protein Science : a Publication of the Protein Society·Q ZhengC DeLisi
Apr 1, 1993·Protein Engineering·P E BoscottW G Richards
Jun 5, 1993·Journal of Molecular Biology·F EisenmengerR Abagyan

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Citations

Oct 30, 2008·Protein Engineering, Design & Selection : PEDS·Meng CuiRoman Osman
Oct 25, 2000·Protein Science : a Publication of the Protein Society·A FiserA Sali
Jul 6, 2010·Proteins·Benjamin D SellersMatthew P Jacobson
Dec 14, 2011·Proteins·Chittaranjan TripathyBruce Randall Donald
Feb 27, 2010·Proteins·Matthew L Danielson, Markus A Lill
Sep 15, 2006·Journal of Computer-aided Molecular Design·Sandhya KortagereErnest L Mehler
May 2, 2002·Protein Engineering·Silvio C E TosattoReinhard Männer
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·M A Martí-RenomA Sali
Aug 1, 1995·Current Opinion in Biotechnology·A Sali

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